Jared Wilkening
Jared Wilkening
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The metagenomics RAST server–a public resource for the automatic phylogenetic and functional analysis of metagenomes
F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, ...
BMC bioinformatics 9 (1), 1-8, 2008
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
modENCODE Consortium, S Roy, J Ernst, PV Kharchenko, P Kheradpour, ...
Science 330 (6012), 1787-1797, 2010
Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes
EM Glass, J Wilkening, A Wilke, D Antonopoulos, F Meyer
Cold Spring Harbor Protocols 2010 (1), pdb. prot5368, 2010
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
A Wilke, T Harrison, J Wilkening, D Field, EM Glass, N Kyrpides, ...
BMC bioinformatics 13, 1-5, 2012
Using clouds for metagenomics: a case study
J Wilkening, A Wilke, N Desai, F Meyer
2009 IEEE International Conference on Cluster Computing and Workshops, 1-6, 2009
A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE
KP Keegan, WL Trimble, J Wilkening, A Wilke, T Harrison, M D'Souza, ...
PLoS computational biology 8 (6), e1002541, 2012
A RESTful API for accessing microbial community data for MG-RAST
A Wilke, J Bischof, T Harrison, T Brettin, M D'Souza, W Gerlach, ...
PLoS computational biology 11 (1), e1004008, 2015
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal
WL Trimble, KP Keegan, M D’Souza, A Wilke, J Wilkening, J Gilbert, ...
BMC bioinformatics 13, 1-10, 2012
Connecting genotype to phenotype in the era of high-throughput sequencing
CS Henry, R Overbeek, F Xia, AA Best, E Glass, J Gilbert, P Larsen, ...
Biochimica et Biophysica Acta (BBA)-General Subjects 1810 (10), 967-977, 2011
A scalable data analysis platform for metagenomics
W Tang, J Wilkening, N Desai, W Gerlach, A Wilke, F Meyer
2013 IEEE International Conference on Big Data, 21-26, 2013
A metagenomics portal for a democratized sequencing world
A Wilke, EM Glass, D Bartels, J Bischof, D Braithwaite, M D’Souza, ...
Methods in Enzymology 531, 487-523, 2013
An experience report: porting the MG‐RAST rapid metagenomics analysis pipeline to the cloud
A Wilke, J Wilkening, EM Glass, NL Desai, F Meyer
Concurrency and Computation: Practice and Experience 23 (17), 2250-2257, 2011
MG-RAST technical report and manual for version 3.3. 6–Rev 1
A Wilke, E Glass, J Bischof, D Braithwaite, M Souza, W Gerlach
Lemont, IL: Argonne National Laboratory, 2013
Shock: active storage for multicloud streaming data analysis
J Bischof, A Wilke, W Gerlach, T Harrison, T Paczian, W Tang, W Trimble, ...
2015 IEEE/ACM 2nd International Symposium on Big Data Computing (BDC), 68-72, 2015
MG-RAST Manural for version 3.6, revision 3
A Wilke, EM Glass, J Bischof, D Braithwaite, W Gerlach, T Harrison, ...
MGRAST, 2015
Report of the 13th Genomic Standards Consortium Meeting, Shenzhen, China, March 4–7, 2012
JA Gilbert, Y Bao, H Wang, SA Sansone, SC Edmunds, N Morrison, ...
Standards in Genomic Sciences 6 (2), 276-286, 2012
Building scalable data management and analysis infrastructure for metagenomics
W Tang, J Wilkening, J Bischof, W Gerlach, A Wilke, N Desai, F Meyer
5th International Workshop on Data-Intensive Computing in the Clouds, Poster …, 2013
North American soil metagenomes cluster by ecosystem type and edaphic factors
DA Antonopoulos, SL O’Brien, KP Keegan, A Amarr, BS Bates, JM Brulc, ...
Science (in preparation), 0
Molecular methods for biofilms
I Ferrera, V Balagué, CR Voolstra, M Aranda, T Bayer, RMM Abed, ...
Biofouling Methods, 87-137, 2014
Section 4 Metagenomics
SM Owens, J Wilkening, JL Fessler, JA Gilbert
Biofouling Methods, 125, 2014
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